322 Works

Research data supporting \"The Missing N1 or Jittered P2: Electrophysiological Correlates of Pattern-Glare in the Time and Frequency Domai\"n

Austyn Tempesta, Claire E. Miller, Vladimir Litvak, Howard Bowman & Andrew Schofield

Borehole and transmissivity dataset, Uganda

Michael Owor, Joseph Okullo, Helen C Fallas, Alan M MacDonald, Donald John MacAllister & Richard Taylor
This dataset comprises 655 borehole records and previously unanalysed pumping tests from across Uganda that were compiled from historical borehole records held within 9 district water offices. The dataset is a compilation of historical borehole records held within nine district water offices across Uganda. These data originated from numerous drilling campaigns undertaken by private contractors in each district to site and construct hand-pump borehole community water supplies between 2000 to 2018. In total over 1000...

Asynchronous Saturation of the Carbon Sink in African and Amazonian tropical forests

Wannes Hubau, Simon Lewis, Oliver Phillips, Kofi Kofi Affum-Baffoe, Hans Hans Beeckman, Aida Cuni-Sanchez, Corneille Ewango, Sophie Fauset, Douglas Sheil, Bonaventure Sonké, Martin Sullivan, Terry Sunderland, Sean Thomas, Katharine Abernethy, Stephen Adu-Bredu, Christian Amani, Timothy Baker, Lindsay Banin, Fidèle Baya, Serge Begne, Amy Bennett, Fabrice Benedet, Robert Bitariho & Yannick Bocko
Data and R-code from Hubau W et al. 2020. 'Asynchronous Saturation of the Carbon Sink in African and Amazonian tropical forests'. Nature 579, 80-87. 2020. DOI: 10.1038/s41586-020-2035-0. ABSTRACT: Structurally intact tropical forests sequestered ~50% of global terrestrial carbon uptake over the 1990s and early 2000s, offsetting ~15% of anthropogenic CO2 emissions1-3. Climate-driven vegetation models typically predict that this tropical forest ‘carbon sink’ will continue for decades4,5. However, recent inventories of intact Amazonian forests show declining...

Data from: The sound of recovery: coral reef restoration success is detectable in the soundscape

Timothy Lamont, Ben Williams, Lucille Chapuis, Mochyudho Prasetya, Marie Seraphim, Harry Harding, Eleanor May, Noel Janetski, Jamaluddin Jompa, Dave Smith, Andrew Radford & Stephen Simpson
1. Pantropical degradation of coral reefs is prompting considerable investment in their active restoration. However, current measures of restoration success are based largely on coral cover, which does not fully reflect ecosystem function or reef health. 2. Soundscapes are an important aspect of reef health; loud and diverse soundscapes guide the recruitment of reef organisms, but this process is compromised when degradation denudes soundscapes. As such, acoustic recovery is a functionally important component of ecosystem...

Palaeolimnological data from 5 Arctic lakes in Greenland, Alaska and Norway [Lakes and Arctic Carbon]

E.J. Whiteford, E. Hopla, N. Solovieva, J. Swales, S. Turner, M. Van Hardenbroek, E. Wiik, M.E. Edwards, V.J. Jones, P.G. Langdon, S. McGowan & N.J. Anderson
This dataset contains palaeolimnological data from sediment cores taken from five Arctic lakes. Two lakes located in Alaska were cored in July 2013, one lake located in Greenland was cored in April 2013, and two lakes located in Norway were cored in March 2014. The data includes macrofossil, chironomids and Cladocera analysis at 2 cm resolution; and loss on ignition, diatoms, biogenic silica, nitrogen and carbon isotopes, algal photosynthetic pigments and pollen analyses at 1...

Zircon U-Pb Sediment provenance data for Miocene to recent sediments collected at Site U1521 during International Ocean Discovery Programme (IODP) Expedition 374 to the Ross Sea, Antarctica

Pieter Vermeesch, Andy Carter & James Marschalek
This dataset comprises zircon U-Pb data on 11 samples, each containing ~90-150 individual grains. This method was applied to sediment samples from IODP Expedition 374 Site U1521 to the Ross Sea, collected on the RV JOIDES Resolution. Shipboard biostratigraphy and magnetostratigraphy suggests the samples are mainly early Miocene in age (McKay et al., 2019). The uppermost samples do, however, include younger Plio-Pleistocene sediments. Samples were measured using an Agilent 7900 laser ablation inductively-coupled plasma mass...

Data from: Extreme behavioural shifts by baboons exploiting risky, resource-rich, human-modified environments

Gaelle Fehlmann, M. Justin O’Riain, Catherine Kerr-Smith, Stephen Hailes, Adrian Luckman, Emily L. C. Shepard & Andrew J. King
A range of species exploit anthropogenic food resources in behaviour known as ‘raiding’. Such behavioural flexibility is considered a central component of a species’ ability to cope with human-induced environmental changes. Here, we study the behavioural processes by which raiding male chacma baboons (Papio ursinus) exploit the opportunities and mitigate the risks presented by raiding in the suburbs of Cape Town, South Africa. Ecological sampling and interviews conducted with ‘rangers’ (employed to manage the baboons’...

Data from: Impact of person-centred care training and person-centred activities on quality of life, agitation, and antipsychotic use in people with dementia living in nursing homes: a cluster-randomised controlled trial

Clive Ballard, Anne Corbett, Martin Orrell, Gareth Williams, Esme Moniz-Cook, Renee Romeo, Bob Woods, Lucy Garrod, Ingelin Testad, Barbara Woodward-Carlton, Jennifer Wenborn, Martin Knapp & Jane Fossey
Background: Agitation is a common, challenging symptom affecting large numbers of people with dementia and impacting on quality of life (QoL). There is an urgent need for evidence-based, cost-effective psychosocial interventions to improve these outcomes, particularly in the absence of safe, effective pharmacological therapies. This study aimed evaluate the efficacy of a person-centered care and psychosocial intervention (WHELD) on QoL, agitation and antipsychotic use in people with dementia living in nursing homes, and to determine...

Data from: Diet quality determines interspecific parasite interactions in host populations

Benjamin Lange, Max Reuter, Dieter Ebert, Koenraad Muylaert & Ellen Decaestecker
The widespread occurrence of multiple infections and the often vast range of nutritional resources for their hosts allow that interspecific parasite interactions in natural host populations might be determined by host diet quality. Nevertheless, the role of diet quality with respect to multispecies parasite interactions on host population level is not clear. We here tested the effect of host population diet quality on the parasite community in an experimental study using Daphnia populations. We studied...

Data from: Polygyny without wealth: popularity in gift games predicts polygyny in BaYaka Pygmies

Nikhil Chaudhary, Gul Deniz Salali, James Thompson, Mark Dyble, Abigail Page, Daniel Smith, Ruth Mace & Andrea Bamberg Migliano
The occurrence of polygynous marriage in hunter–gatherer societies, which do not accumulate wealth, remains largely unexplored since resource availability is dependent on male hunting capacity and limited by the lack of storage. Hunter–gatherer societies offer the greatest insight in to human evolution since they represent the majority of our species' evolutionary history. In order to elucidate the evolution of hunter–gatherer polygyny, we study marriage patterns of BaYaka Pygmies. We investigate (i) rates of polygyny among...

Data from: Community water improvement, household water insecurity, and women’s psychological distress: an intervention and control study in Ethiopia

Edward G. J. Stevenson, Argaw Ambelu, Bethany A. Caruso, Yihenew Tesfaye & Matthew C. Freeman
Background: Over 650 million people worldwide lack access to safe water supplies, and even among those who have gained access to ‘improved’ sources, water may be seasonally unreliable, far from homes, expensive, and provide insufficient quantity. Measurement of water access at the level of communities and households remains crude, and better measures of household water insecurity are urgently needed to inform needs assessments and monitoring and evaluation. We set out to assess the validity of...

Data from: Direct evidence for encoding of motion streaks in human visual cortex

Deborah Apthorp, D. Samuel Schwarzkopf, Christian Kaul, Bahador Bahrami, David Alais & Geraint Rees
Temporal integration in the visual system causes fast-moving objects to generate static, oriented traces (‘motion streaks’), which could be used to help judge direction of motion. While human psychophysics and single-unit studies in non-human primates are consistent with this hypothesis, direct neural evidence from the human cortex is still lacking. First, we provide psychophysical evidence that faster and slower motions are processed by distinct neural mechanisms: faster motion raised human perceptual thresholds for static orientations...

Data from: Anthropogenic and ecological drivers of amphibian disease (Ranavirosis)

Alexandra C. North, David J. Hodgson, Stephen J. Price & Amber G. F. Griffiths
Ranaviruses are causing mass amphibian die-offs in North America, Europe and Asia, and have been implicated in the decline of common frog (Rana temporaria) populations in the UK. Despite this, we have very little understanding of the environmental drivers of disease occurrence and prevalence. Using a long term (1992-2000) dataset of public reports of amphibian mortalities, we assess a set of potential predictors of the occurrence and prevalence of Ranavirus-consistent common frog mortality events in...

Data from: Paleo-islands as refugia and sources of genetic diversity within volcanic archipelagos: The case of the widespread endemic Canarina canariensis (Campanulaceae)

Mario Mairal, Isabel Sanmartín, Juan José Aldasoro, Victoria Culshaw, Ioanna Manolopoulou & Marisa Alarcón
Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the...

Data from: The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

Vienna Kowallik, Eric Miller & Duncan Greig
The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high-throughput...

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

Data from: Genetic drift in antagonistic genes leads to divergence in sex-specific fitness between experimental populations of Drosophila melanogaster

Jack Hesketh, Kevin Fowler & Max Reuter
Males and females differ in their reproductive roles and as a consequence are often under diverging selection pressures on shared phenotypic traits. Theory predicts that divergent selection can favor the invasion of sexually antagonistic alleles, which increase the fitness of one sex at the detriment of the other. Sexual antagonism can be subsequently resolved through the evolution of sex-specific gene expression, allowing the sexes to diverge phenotypically. While sexual dimorphism is very common, recent evidence...

Data from: The Chord-Normalized Expected Species Shared (CNESS)-distance represents a superior measure of species turnover patterns

Yi Zou & Jan Axmacher
1. Measures of β-diversity characterizing the difference in species composition between samples are commonly used in ecological studies. Nonetheless, commonly used dissimilarity measures require high sample completeness, or at least similar sample sizes between samples. In contrast, the Chord-Normalized Expected Species Shared (CNESS) dissimilarity measure calculates the probability of collecting the same set of species in random samples of a standardized size, and hence is not sensitive to completeness or size of compared samples. To...

Linking socioeconomic inequalities and type 2 diabetes through obesity and lifestyle factors among Mexican adults: a structural equations modeling approach

Edgar Denova-Gutiérrez, Delfino Vargas-Chanes, Sheyla Hernández, David Napier, Simón Barquera & Paloma Muñoz-Aguirre
Objective. To assess the association between type 2 dia­betes (DM2) and socioeconomic inequalities, mediated by the contribution of body mass index (BMI), physical activity (PA), and diet (diet-DII). Materials and methods. We conducted a cross-sectional analysis using data of adults participating in the Diabetes Mellitus Survey of Mexico City. Socioeconomic and demographic characteristics as well as height and weight, dietary intake, leisure time activity and the presence of DM2 were measured. We fitted a structural...

Data from: Spatiotemporal variation in completeness of the early cynodont fossil record and its implications for mammalian evolutionary history

Grace Varnham, Philip Mannion & Christian Kammerer
Mammals are the only surviving group of Cynodontia, a synapsid clade that first appears in the fossil record in the late Permian, ~260 million years ago. Here, using three metrics that capture skeletal completeness, we quantify the quality of the early cynodont fossil record in time and space to evaluate the impact of sampling and preservational biases on our understanding of the group’s evolutionary history. There is no consistent global sampling signal for early cynodonts....

RepeatModeler and RepeatMasker output files

Reuben Nowell, Christopher Wilson, Pedro Almeida, Philipp Schiffer, Diego Fontaneto, Lutz Becks, Fernando Rodriguez, Irina Arkhipova & Timothy Barraclough
Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active...

Defining species when there is gene flow

Ziheng Yang & Xiyun Jiao
Whatever one’s definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with migration or introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising...

The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases

Roger Close, Roger Benson, John Alroy, Matthew Carrano, Terri Cleary, Emma Dunne, Philip Mannion, Mark Uhen & Richard Butler
There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 38,711 fossil occurrences, we show that the spatial extent of the ‘global’ terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic, and that this spatial variation explains around 75% of the variation in known fossil species counts. Controlling for this bias, we find that regional-scale terrestrial...

Examining the relationship between processing fluency and memory for source information

Tina Huang & David Shanks
Familiarity-based processes such as processing fluency can influence memory judgements in tests of item recognition. Many conventional accounts of source memory assume minimal influence of familiarity on source memory, but recent work has suggested that source memory judgements are affected when test stimuli are processed with greater fluency as a result of priming. The present experiments investigated the relationship between fluency and the accuracy of source memory decisions. Participants studied words presented with different source...

Data from: Nutritional geometry of mitochondrial genetic effects on male fertility

M. Florencia Camus, James Moore & Max Reuter
Organismal fitness is partly determined by how well the nutritional intake matches sex-specific metabolic requirements. Metabolism itself is underpinned by complex genomic interactions involving products from both nuclear and mitochondrial genomes. Products from these two genomes must coordinate how nutrients are extracted, utilised and recycled; processes vital for fuelling reproduction. Given the complicated nature of metabolism, it is not well understood how the functioning of these two genomes is modulated by nutrients. Here we use...

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